tag:blogger.com,1999:blog-4948885059517209129.post3650892571707922507..comments2016-08-22T08:52:11.001-04:00Comments on Quintessence of Dust: Signature in the Cell: Chapters 4 and 5 - errors and problemsStephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.comBlogger8125tag:blogger.com,1999:blog-4948885059517209129.post-47542892973223803692010-06-06T20:03:17.087-04:002010-06-06T20:03:17.087-04:00WRT alternative splicing, it should be noted that ...WRT alternative splicing, it should be noted that a substantial percentage (at least 60%) of human genes are the result of intron fcnality in alternative splicing. (Molecular Cell Biology Sixth Edition pg. 126)<br /><br />Multidomain protiens, for one example, are typical products of this process that play important roles in celluar function and many human disease are the result of mutations wrt to splice site selection. Molecular Cell Biology Sixth Edition pg. 126, pg. 334)Dannoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-12125806178094320872010-02-27T16:27:10.212-05:002010-02-27T16:27:10.212-05:00Hi Prof. Matheson,
You&#39;ve got Mike Gene&#39;...Hi Prof. Matheson, <br /><br />You&#39;ve got Mike Gene&#39;s attention: <br /><br />http://designmatrix.wordpress.com/2010/02/26/introns-and-design/Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-35071800018001562302010-02-24T12:39:27.043-05:002010-02-24T12:39:27.043-05:00&quot;Meyer attempts to construct an analogy betwe...&quot;Meyer attempts to construct an analogy between CAD-CAM and protein synthesis on pages 120-121. It&#39;s a failure, because there&#39;s little analogy between the two processes... &quot;<br /><br />This is so true. When I design a mechanical part to be fabricated, I can take my CAD output and export a data file that a CNC (computer numerical control) lathe or mill can read and translate into a part. Or I can export the model in a stereo-lithography file and have the part &quot;printed&quot; on an RP (rapid prototype) machine.<br /><br />But in either case, if the data become corrupted, the process is terminated. Why? Because of the way the information is translated between formats, read, and interpreted, corrupt data necessarily become nonsensical during the process - which faults the sequence. <br /><br />Now, if a corrupt data file cuased two features to be machined where I had only designed one, or if it swaped one feature with another or slightly modified a feature, then you would have something akin to protein synthesis. But as it stands now, CAD-CAM is absolutly nothing like DNA translation.<br /><br />And like you, as soon as I ready the part about &quot;junk DNA&quot; I lost all interest in the book. And I was honestly enjoying it up to that point.Gordon J. Gloverhttp://www.youtube.com/glovergjnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-75695339596276452582010-02-21T05:32:10.479-05:002010-02-21T05:32:10.479-05:00Thanks for the series, again.Thanks for the series, again.Martin LaBarhttps://www.blogger.com/profile/14629053725732957599noreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-88575806072398317932010-02-15T17:24:57.311-05:002010-02-15T17:24:57.311-05:00Hi Steve-
This series of posts has been quite amus...Hi Steve-<br />This series of posts has been quite amusing and enlightening, having not paid much attention to ID and creationism until recently. I haven&#39;t read SitC, but I&#39;ve skimmed the parts available on amazon. A few things stood out in chapter 5:<br /><br />To add to the list of errors-<br />On page 128, Meyer refers to a &quot;protein within the ribosome known as a peptidyl transferase&quot; performing the actual peptide bond formation reaction. Of course, this is a mistake, avoiding one of the key pieces of evidence for the RNA world: that the peptidyl transferase center of the ribosome is composed entirely of RNA- the ribosome is a ribozyme. It&#39;s not like this is a little known fact, it&#39;s one of the first major discoveries to come from the structure of the ribosome, which earned the Nobel Prize in Chemistry last year. It&#39;s hard to believe Meyer managed to miss it.<br /> <br />Considering one of Meyer&#39;s main points is the chicken/egg problem of translation, you think he might spend at least a little time discussing this point. As far as I can tell, Meyer never explicitly deals with it. The closest he comes is mentioning in the RNA world chapter (pg 304) that rRNA &quot;promotes&quot; peptide bond formation, citing very early biochemical work by Harry Noller from 1992 (long before the ribosome structure). Noller&#39;s biochemical work was critical early evidence for the role of RNA in the ribosome, but it was the structure that confirmed it. Meyer makes it sound like RNA is some cofactor, a claim that, prior to the structure, would still be something of a stretch, but was completely invalidated when the structure showed that RNA forms the entire PT active site.<br /><br />And of course there are countless other problems. One other one that stood out-only a few pages after the peptidyl transferase protein, he claims the aminoacyl synthetases (aaRSs-the proteins that charge tRNAs with their cognate amino acids) all have distinct shapes. Although in some sense their active sites will differ to accommodate the different amino acids, all tRNAs share one of two common structures. There&#39;s a ton of work on tracing the evolutionary history of existing aaRS, suggesting they all descended from 2 common ancestor protein folds. Again, no discussion of this anywhere in the book as far as I can tell, just the assertion that all 20 had to emerge at once for translation to work.<br /><br />Overall, my impression seems to be that Meyer has skimmed the literature, picked out points he has canned responses to, and ignored or managed to remain ignorant of vast swaths of other evidence.Davidhttps://www.blogger.com/profile/05235292977400315650noreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-82282708895220259152010-02-15T13:10:17.529-05:002010-02-15T13:10:17.529-05:00Of course Meyer&#39;s book is written to advance h...Of course Meyer&#39;s book is written to advance his agenda. He may be an IDiot, but he&#39;s not an idiot. Nor is he woefully nor willfully ignorant. Meyer knows exactly what he&#39;s doing.<br /><br />Consider what&#39;s failed for creationists: 2nd law of thermo., irreducible complexity, the explanatory filter, the &quot;edge&quot; of evolution. Nothing&#39;s working for them.<br /><br />Now, they&#39;ve latched on to something pretty obscure out of electrical engineering of all things: information theory. Unfortunately, that&#39;s not working out any better as they get messed up between Shannon and Kolmogorov definitions that apply to different things. <br /><br />Specified information? Please! Why not just call it beautiful and really beautiful because, obviously, merely beautiful isn&#39;t good enough? Either way Meyer is trapped in subjectivity, and his thesis fails.<br /><br />Whatever Meyer writes it&#39;s clear he started with the conclusion, the signature in the cell, and worked backwards to find support however tenuous. He&#39;s very careful to write and slant his writing only to things that support his conclusion. That&#39;s why it appears so much is missing and why there are so many errors. His target audience will neither care nor understand.<br /><br />Ten years from now Meyer will still be touting &quot;junk DNA&quot; just as Behe touts &quot;mousetrap.&quot;<br /><br />Thank you for this continuing review. You&#39;re doing yeoman&#39;s work for the rest of us!Billhttps://www.blogger.com/profile/04921039513056888571noreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-73384478569477035652010-02-15T13:09:04.798-05:002010-02-15T13:09:04.798-05:00Hi Stephen,
To be as fair as possible, a central ...Hi Stephen,<br /><br />To be as fair as possible, a central part of the spliceosome is an endonuclease of a sort - an enzyme (composed of RNA) that breaks the RNA chain so as to permit the removal of the intron.<br /><br />And while I am sure that Meyer is unaware, the processing of ribosomal RNAs does involve exonucleases as well as endonucleases. Not that mixing up the different processing systems can restore any credibility to Meyer, but ...Arthur Hunthttp://www.aghunt.wordpress.comnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-71200589589060482002010-02-15T05:39:16.101-05:002010-02-15T05:39:16.101-05:00Might I suggest that the biologist who Meyer got t...Might I suggest that the biologist who Meyer got to look through his book and to provide him with details was Jonathan Wells?<br /><br />On junk DNA, it would seem that this recent article by Fuz Rana is more of the same.<br /><br />http://www.reasons.org/junk-dna-hotspots-have-evolutionary-biologists-singing-blues<br /><br />The writings of ID advocates in these areas seem to be essentially indistinguishable from those at RTB, AIG, or ICR. Even Richard Sternberg, who Meyer hailed as a &quot;genomics expert,&quot; made these arguments in their recent debate with Prothero and Shermer. He claimed &quot;so-called pseudogenes&quot; have important functions, as do ERVs, and Meyer said that &quot;junk DNA is species specific&quot; (whatever that means) and so is evidence against common descent.Halnoreply@blogger.com